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de Freitas KEJ, dos Santos RS, Busanello C, de Carvalho Victoria F, Lopes JL, Wing RA, de Oliveira AC. Starch Synthesis-Related Genes (SSRG) Evolution in the Genus Oryza. Plants 2021; 10:plants10061057. [PMID: 34070565 PMCID: PMC8229393 DOI: 10.3390/plants10061057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/14/2021] [Accepted: 04/14/2021] [Indexed: 11/18/2022]
Abstract
Cooking quality is an important attribute in Common/Asian rice (Oryzasativa L.) varieties, being highly dependent on grain starch composition. This composition is known to be highly dependent on a cultivar’s genetics, but the way in which their genes express different phenotypes is not well understood. Further analysis of variation of grain quality genes using new information obtained from the wild relatives of rice should provide important insights into the evolution and potential use of these genetic resources. All analyses were conducted using bioinformatics approaches. The analysis of the protein sequences of grain quality genes across the Oryza suggest that the deletion/mutation of amino acids in active sites result in variations that can negatively affect specific steps of starch biosynthesis in the endosperm. On the other hand, the complete deletion of some genes in the wild species may not affect the amylose content. Here we present new insights for Starch Synthesis-Related Genes (SSRGs) evolution from starch-specific rice phenotypes.
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Affiliation(s)
- Karine E. Janner de Freitas
- Centro de desenvolvimento Tecnológico—CDTec, Graduate Program in biotechnology, Capão do Leão Campus, Federal de Pelotas, Pelotas 96160, Brazil; (K.E.J.d.F.); (C.B.); (J.L.L.)
| | | | - Carlos Busanello
- Centro de desenvolvimento Tecnológico—CDTec, Graduate Program in biotechnology, Capão do Leão Campus, Federal de Pelotas, Pelotas 96160, Brazil; (K.E.J.d.F.); (C.B.); (J.L.L.)
| | - Filipe de Carvalho Victoria
- Núcleo de Estudos da Vegetação Antártica—NEVA, Campus São Gabriel Federal do Pampa (UNIPAMPA), São Gabriel 97030, Brazil;
| | - Jennifer Luz Lopes
- Centro de desenvolvimento Tecnológico—CDTec, Graduate Program in biotechnology, Capão do Leão Campus, Federal de Pelotas, Pelotas 96160, Brazil; (K.E.J.d.F.); (C.B.); (J.L.L.)
| | - Rod A. Wing
- The School of Plant Sciences, Ecology & Evolutionary Biology, Arizona Genomics Institute, Tucson, AZ 97030, USA;
- Center for Desert Agriculture, King Abdullah University of Science & Technology, Thuwal 23955, Saudi Arabia
| | - Antonio Costa de Oliveira
- Centro de desenvolvimento Tecnológico—CDTec, Graduate Program in biotechnology, Capão do Leão Campus, Federal de Pelotas, Pelotas 96160, Brazil; (K.E.J.d.F.); (C.B.); (J.L.L.)
- Correspondence:
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Li D, Yang Z, Liu X, Song Z, Feng Z, He Y. Cloning and expression analysis of cDNAs encoding ADP-glucose pyrophosphorylase large and small subunits from hulless barley (Hordeum vulgare L. var. nudum). ACTA ACUST UNITED AC 2019; 73:191-197. [PMID: 29455192 DOI: 10.1515/znc-2017-0154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 01/20/2018] [Indexed: 11/15/2022]
Abstract
As an important plateau cereal crop, hulless barley is the principal food for the Tibetan people in China. ADP-glucose pyrophosphorylase (AGPase) is considered as the key enzyme for starch biosynthesis in plants. In this study, cDNAs encoding the small subunit (SSU I) and large subunit (LSU I) of AGPase were isolated from hulless barley. The results showed that SSU I and LSU I were 1438 and 1786 bp in length with a complete open reading frame (ORF) of 1419 and 1572 bp. The ORF-encoded polypeptides of 472 and 523 amino acids were having calculated molecular masses of 52.01 and 58.23 kDa, and the pI values were 5.59 and 6.30. In addition, phylogenetic analysis showed that SSU I and LSU I had the same phylogenetic trends with some species. Furthermore, expression levels in different growth periods and tissues of two hulless barley varieties were analyzed by quantitative reverse transcription-polymerase chain reaction. Gene expression levels of SSU I and LSU I were consistent with the total starch accumulation rate in endosperm. In conclusion, our data confirmed that SSU I and LSU I played an important role in hulless barley starch synthesis.
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Affiliation(s)
- Dongmei Li
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, P.R. China
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P.R. China
| | - Zhimin Yang
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Xinchun Liu
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Zhen Song
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P.R. China
| | - Zongyun Feng
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, P.R. China
| | - Yang He
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P.R. China
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Batra R, Saripalli G, Mohan A, Gupta S, Gill KS, Varadwaj PK, Balyan HS, Gupta PK. Comparative Analysis of AGPase Genes and Encoded Proteins in Eight Monocots and Three Dicots with Emphasis on Wheat. Front Plant Sci 2017; 8:19. [PMID: 28174576 PMCID: PMC5259687 DOI: 10.3389/fpls.2017.00019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 01/04/2017] [Indexed: 05/11/2023]
Abstract
ADP-glucose pyrophosphorylase (AGPase) is a heterotetrameric enzyme with two large subunits (LS) and two small subunits (SS). It plays a critical role in starch biosynthesis. We are reporting here detailed structure, function and evolution of the genes encoding the LS and the SS among monocots and dicots. "True" orthologs of maize Sh2 (AGPase LS) and Bt2 (AGPase SS) were identified in seven other monocots and three dicots; structure of the enzyme at protein level was also studied. Novel findings of the current study include the following: (i) at the DNA level, the genes controlling the SS are more conserved than those controlling the LS; the variation in both is mainly due to intron number, intron length and intron phase distribution; (ii) at protein level, the SS genes are more conserved relative to those for LS; (iii) "QTCL" motif present in SS showed evolutionary differences in AGPase belonging to wheat 7BS, T. urartu, rice and sorghum, while "LGGG" motif in LS was present in all species except T. urartu and chickpea; SS provides thermostability to AGPase, while LS is involved in regulation of AGPase activity; (iv) heterotetrameric structure of AGPase was predicted and analyzed in real time environment through molecular dynamics simulation for all the species; (v) several cis-acting regulatory elements were identified in the AGPase promoters with their possible role in regulating spatial and temporal expression (endosperm and leaf tissue) and also the expression, in response to abiotic stresses; and (vi) expression analysis revealed downregulation of both subunits under conditions of heat and drought stress. The results of the present study have allowed better understanding of structure and evolution of the genes and the encoded proteins and provided clues for exploitation of variability in these genes for engineering thermostable AGPase.
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Affiliation(s)
- Ritu Batra
- Bioinformatics Infrastructure Facility (BIF) Laboratory, Department of Genetics and Plant Breeding, Ch. Charan Singh UniversityMeerut, India
| | - Gautam Saripalli
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Ch. Charan Singh UniversityMeerut, India
| | - Amita Mohan
- Department of Crop and Soil Sciences, Washington State UniversityPullman, WA, USA
| | - Saurabh Gupta
- Department of Bioinformatics, Indian Institute of Information Technology-AllahabadAllahabad, India
| | - Kulvinder S. Gill
- Department of Crop and Soil Sciences, Washington State UniversityPullman, WA, USA
- *Correspondence: Kulvinder S. Gill
| | - Pritish K. Varadwaj
- Department of Bioinformatics, Indian Institute of Information Technology-AllahabadAllahabad, India
| | - Harindra S. Balyan
- Bioinformatics Infrastructure Facility (BIF) Laboratory, Department of Genetics and Plant Breeding, Ch. Charan Singh UniversityMeerut, India
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Ch. Charan Singh UniversityMeerut, India
| | - Pushpendra K. Gupta
- Bioinformatics Infrastructure Facility (BIF) Laboratory, Department of Genetics and Plant Breeding, Ch. Charan Singh UniversityMeerut, India
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Jourda C, Cardi C, Gibert O, Giraldo Toro A, Ricci J, Mbéguié-A-Mbéguié D, Yahiaoui N. Lineage-Specific Evolutionary Histories and Regulation of Major Starch Metabolism Genes during Banana Ripening. Front Plant Sci 2016; 7:1778. [PMID: 27994606 PMCID: PMC5133247 DOI: 10.3389/fpls.2016.01778] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/11/2016] [Indexed: 05/24/2023]
Abstract
Starch is the most widespread and abundant storage carbohydrate in plants. It is also a major feature of cultivated bananas as it accumulates to large amounts during banana fruit development before almost complete conversion to soluble sugars during ripening. Little is known about the structure of major gene families involved in banana starch metabolism and their evolution compared to other species. To identify genes involved in banana starch metabolism and investigate their evolutionary history, we analyzed six gene families playing a crucial role in plant starch biosynthesis and degradation: the ADP-glucose pyrophosphorylases (AGPases), starch synthases (SS), starch branching enzymes (SBE), debranching enzymes (DBE), α-amylases (AMY) and β-amylases (BAM). Using comparative genomics and phylogenetic approaches, these genes were classified into families and sub-families and orthology relationships with functional genes in Eudicots and in grasses were identified. In addition to known ancestral duplications shaping starch metabolism gene families, independent evolution in banana and grasses also occurred through lineage-specific whole genome duplications for specific sub-families of AGPase, SS, SBE, and BAM genes; and through gene-scale duplications for AMY genes. In particular, banana lineage duplications yielded a set of AGPase, SBE and BAM genes that were highly or specifically expressed in banana fruits. Gene expression analysis highlighted a complex transcriptional reprogramming of starch metabolism genes during ripening of banana fruits. A differential regulation of expression between banana gene duplicates was identified for SBE and BAM genes, suggesting that part of starch metabolism regulation in the fruit evolved in the banana lineage.
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Affiliation(s)
- Cyril Jourda
- CIRAD, UMR AGAPMontpellier, France
- CIRAD, UMR PVBMTSaint-Pierre, France
| | | | - Olivier Gibert
- CIRAD, UMR QUALISUDMontpellier, France
- CIRAD, UMR QUALISUDJakarta, Indonesia
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Saripalli G, Gupta PK. AGPase: its role in crop productivity with emphasis on heat tolerance in cereals. Theor Appl Genet 2015; 128:1893-916. [PMID: 26152573 DOI: 10.1007/s00122-015-2565-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 06/16/2015] [Indexed: 05/11/2023]
Abstract
AGPase, a key enzyme of starch biosynthetic pathway, has a significant role in crop productivity. Thermotolerant variants of AGPase in cereals may be used for developing cultivars, which may enhance productivity under heat stress. Improvement of crop productivity has always been the major goal of plant breeders to meet the global demand for food. However, crop productivity itself is influenced in a large measure by a number of abiotic stresses including heat, which causes major losses in crop productivity. In cereals, crop productivity in terms of grain yield mainly depends upon the seed starch content so that starch biosynthesis and the enzymes involved in this process have been a major area of investigation for plant physiologists and plant breeders alike. Considerable work has been done on AGPase and its role in crop productivity, particularly under heat stress, because this enzyme is one of the major enzymes, which catalyses the rate-limiting first committed key enzymatic step of starch biosynthesis. Keeping the above in view, this review focuses on the basic features of AGPase including its structure, regulatory mechanisms involving allosteric regulators, its sub-cellular localization and its genetics. Major emphasis, however, has been laid on the genetics of AGPases and its manipulation for developing high yielding cultivars that will have comparable productivity under heat stress. Some important thermotolerant variants of AGPase, which mainly involve specific amino acid substitutions, have been highlighted, and the prospects of using these thermotolerant variants of AGPase in developing cultivars for heat prone areas have been discussed. The review also includes a brief account on transgenics for AGPase, which have been developed for basic studies and crop improvement.
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Affiliation(s)
- Gautam Saripalli
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India
| | - Pushpendra Kumar Gupta
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India.
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Abstract
AGPase, a key enzyme of starch biosynthetic pathway, has a significant role in crop productivity. Thermotolerant variants of AGPase in cereals may be used for developing cultivars, which may enhance productivity under heat stress. Improvement of crop productivity has always been the major goal of plant breeders to meet the global demand for food. However, crop productivity itself is influenced in a large measure by a number of abiotic stresses including heat, which causes major losses in crop productivity. In cereals, crop productivity in terms of grain yield mainly depends upon the seed starch content so that starch biosynthesis and the enzymes involved in this process have been a major area of investigation for plant physiologists and plant breeders alike. Considerable work has been done on AGPase and its role in crop productivity, particularly under heat stress, because this enzyme is one of the major enzymes, which catalyses the rate-limiting first committed key enzymatic step of starch biosynthesis. Keeping the above in view, this review focuses on the basic features of AGPase including its structure, regulatory mechanisms involving allosteric regulators, its sub-cellular localization and its genetics. Major emphasis, however, has been laid on the genetics of AGPases and its manipulation for developing high yielding cultivars that will have comparable productivity under heat stress. Some important thermotolerant variants of AGPase, which mainly involve specific amino acid substitutions, have been highlighted, and the prospects of using these thermotolerant variants of AGPase in developing cultivars for heat prone areas have been discussed. The review also includes a brief account on transgenics for AGPase, which have been developed for basic studies and crop improvement.
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Affiliation(s)
- Gautam Saripalli
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India
| | - Pushpendra Kumar Gupta
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India.
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Saripalli G, Gupta PK. AGPase: its role in crop productivity with emphasis on heat tolerance in cereals. Theor Appl Genet 2015; 128:1893-1916. [PMID: 26152573 DOI: 10.1007/s00122-015-25652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 06/16/2015] [Indexed: 05/26/2023]
Abstract
AGPase, a key enzyme of starch biosynthetic pathway, has a significant role in crop productivity. Thermotolerant variants of AGPase in cereals may be used for developing cultivars, which may enhance productivity under heat stress. Improvement of crop productivity has always been the major goal of plant breeders to meet the global demand for food. However, crop productivity itself is influenced in a large measure by a number of abiotic stresses including heat, which causes major losses in crop productivity. In cereals, crop productivity in terms of grain yield mainly depends upon the seed starch content so that starch biosynthesis and the enzymes involved in this process have been a major area of investigation for plant physiologists and plant breeders alike. Considerable work has been done on AGPase and its role in crop productivity, particularly under heat stress, because this enzyme is one of the major enzymes, which catalyses the rate-limiting first committed key enzymatic step of starch biosynthesis. Keeping the above in view, this review focuses on the basic features of AGPase including its structure, regulatory mechanisms involving allosteric regulators, its sub-cellular localization and its genetics. Major emphasis, however, has been laid on the genetics of AGPases and its manipulation for developing high yielding cultivars that will have comparable productivity under heat stress. Some important thermotolerant variants of AGPase, which mainly involve specific amino acid substitutions, have been highlighted, and the prospects of using these thermotolerant variants of AGPase in developing cultivars for heat prone areas have been discussed. The review also includes a brief account on transgenics for AGPase, which have been developed for basic studies and crop improvement.
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Affiliation(s)
- Gautam Saripalli
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India
| | - Pushpendra Kumar Gupta
- Molecular Biology Laboratory, Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India.
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Yang Z, Wang Y, Gao Y, Zhou Y, Zhang E, Hu Y, Yuan Y, Liang G, Xu C. Adaptive evolution and divergent expression of heat stress transcription factors in grasses. BMC Evol Biol 2014; 14:147. [PMID: 24974883 PMCID: PMC4094458 DOI: 10.1186/1471-2148-14-147] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 06/20/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Heat stress transcription factors (Hsfs) regulate gene expression in response to heat and many other environmental stresses in plants. Understanding the adaptive evolution of Hsf genes in the grass family will provide potentially useful information for the genetic improvement of modern crops to handle increasing global temperatures. RESULTS In this work, we performed a genome-wide survey of Hsf genes in 5 grass species, including rice, maize, sorghum, Setaria, and Brachypodium, by describing their phylogenetic relationships, adaptive evolution, and expression patterns under abiotic stresses. The Hsf genes in grasses were divided into 24 orthologous gene clusters (OGCs) based on phylogeneitc relationship and synteny, suggesting that 24 Hsf genes were present in the ancestral grass genome. However, 9 duplication and 4 gene-loss events were identified in the tested genomes. A maximum-likelihood analysis revealed the effects of positive selection in the evolution of 11 OGCs and suggested that OGCs with duplicated or lost genes were more readily influenced by positive selection than other OGCs. Further investigation revealed that positive selection acted on only one of the duplicated genes in 8 of 9 paralogous pairs, suggesting that neofunctionalization contributed to the evolution of these duplicated pairs. We also investigated the expression patterns of rice and maize Hsf genes under heat, salt, drought, and cold stresses. The results revealed divergent expression patterns between the duplicated genes. CONCLUSIONS This study demonstrates that neofunctionalization by changes in expression pattern and function following gene duplication has been an important factor in the maintenance and divergence of grass Hsf genes.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Chenwu Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China.
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Nougué O, Corbi J, Ball SG, Manicacci D, Tenaillon MI. Molecular evolution accompanying functional divergence of duplicated genes along the plant starch biosynthesis pathway. BMC Evol Biol 2014; 14:103. [PMID: 24884572 PMCID: PMC4041918 DOI: 10.1186/1471-2148-14-103] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 05/02/2014] [Indexed: 12/15/2022] Open
Abstract
Background Starch is the main source of carbon storage in the Archaeplastida. The starch biosynthesis pathway (sbp) emerged from cytosolic glycogen metabolism shortly after plastid endosymbiosis and was redirected to the plastid stroma during the green lineage divergence. The SBP is a complex network of genes, most of which are members of large multigene families. While some gene duplications occurred in the Archaeplastida ancestor, most were generated during the sbp redirection process, and the remaining few paralogs were generated through compartmentalization or tissue specialization during the evolution of the land plants. In the present study, we tested models of duplicated gene evolution in order to understand the evolutionary forces that have led to the development of SBP in angiosperms. We combined phylogenetic analyses and tests on the rates of evolution along branches emerging from major duplication events in six gene families encoding sbp enzymes. Results We found evidence of positive selection along branches following cytosolic or plastidial specialization in two starch phosphorylases and identified numerous residues that exhibited changes in volume, polarity or charge. Starch synthases, branching and debranching enzymes functional specializations were also accompanied by accelerated evolution. However, none of the sites targeted by selection corresponded to known functional domains, catalytic or regulatory. Interestingly, among the 13 duplications tested, 7 exhibited evidence of positive selection in both branches emerging from the duplication, 2 in only one branch, and 4 in none of the branches. Conclusions The majority of duplications were followed by accelerated evolution targeting specific residues along both branches. This pattern was consistent with the optimization of the two sub-functions originally fulfilled by the ancestral gene before duplication. Our results thereby provide strong support to the so-called “Escape from Adaptive Conflict” (EAC) model. Because none of the residues targeted by selection occurred in characterized functional domains, we propose that enzyme specialization has occurred through subtle changes in affinity, activity or interaction with other enzymes in complex formation, while the basic function defined by the catalytic domain has been maintained.
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Affiliation(s)
| | | | | | - Domenica Manicacci
- University Paris-Sud, UMR 0320/UMR 8120 Génétique Végétale, Ferme du Moulon, F-91190 Gif-sur-Yvette, France.
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Mahendhiran M, Ramirez-Prado JH, Escobedo-Gracia Medrano RM, Canto-Canché B, Tzec-Simá M, Grijalva-Arango R, James-Kay A. Single nucleotide polymorphisms in partial sequences of the gene encoding the large sub-units of ADP-glucose pyrophosphorylase within a representative collection of 10 Musa genotypes. ELECTRON J BIOTECHN 2014. [DOI: 10.1016/j.ejbt.2014.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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